title: Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea.
abstract: For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.
authors.affiliation: International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Narihiro
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sekiguchi
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D015373:Bacterial Typing Techniques / Q000295:instrumentation / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D015342:DNA Probes / Q000235:genetics; D004783:Environmental Microbiology; D008697:Methane / Q000378:metabolism*; D015336:Molecular Probe Techniques / Q000295:instrumentation; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D017931:DNA Primers; D015342:DNA Probes; D008697:Methane